RetrogeneDB ID: retro_opri_1088

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_692:179802..180214(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: EIF4E1B
• Ensembl ID: ENSOPRG00000008875
• Aliases: None
• Description: eukaryotic translation initiation factor 4E family member 1B [Source:HGNC Symbol;Acc:33179]

Sequence

>retro_opri_1088
AGGTGGGCTCTGTGGTTCTTCAAGAATGACCGCAGCCGGGCCTGGCATGACAACCTGCAACTGGTCACCAAGGTGGACAC
TGTGGAGGACTTGTGGGCGATGTACAGTCACATCCAGCTAGCCAGCAAGCTCTCCAGTGGCTGTGACTATGTGCTGTTCA
AGGATGGCATCGAGCCCATGTGGGAAGACAGCAGGAACAAGTGGGTGGCCGCTGGCTCATGAGCCTGGCCAAGCAACAGC
GCCACAGTGAGCTGGACAGACTGTGGCTGGAGACGCTGCTGTGTCTGATGGGGAGAGCTTTGAGGAGCACAGCAGGGAGG
TGTGTGGAGCTGTACTTAACATCCGCACCAAAGGGGACAAGATTGCTGTTTGGACCCGGGAGGCTGAGAACCAGACAGGC
GTGCTGCACATC

Alignment

ORF - retro_opri_1088 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.71 %
• Parental protein coverage: 92. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RWALWFFKNDRSRAWHDNLQLVTKVDTVEDFWAMYSHIQLASKLSSGCDYALFKDGIEPMWEDSRNK-RG
          RWALWFFKNDRSRAWHDNLQLVTKVDTVED.WAMYSHIQLASKLSSGCDY.LFKDGIEPMWEDSRNK..G
Retrocopy RWALWFFKNDRSRAWHDNLQLVTKVDTVEDLWAMYSHIQLASKLSSGCDYVLFKDGIEPMWEDSRNK<VG

Parental  GRWLMSLAKQQRHSELDRLWLETLLCLI-GESFEEHSREVCGAVLNIRTKGDKIAVWTREAENQTGVLHI
          GRWLMSLAKQQRHSELDRLWLETLLCL..GESFEEHSREVCGAVLNIRTKGDKIAVWTREAENQTGVLHI
Retrocopy GRWLMSLAKQQRHSELDRLWLETLLCLM<GESFEEHSREVCGAVLNIRTKGDKIAVWTREAENQTGVLHI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_1088 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003103	1 retrocopy	retro_btau_1679,
Erinaceus europaeus	ENSEEUG00000005920	1 retrocopy	retro_eeur_414,
Loxodonta africana	ENSLAFG00000027919	1 retrocopy	retro_lafr_866,
Monodelphis domestica	ENSMODG00000005097	3 retrocopies	retro_mdom_1779, retro_mdom_47, retro_mdom_710,
Mus musculus	ENSMUSG00000074895	1 retrocopy	retro_mmus_510,
Nomascus leucogenys	ENSNLEG00000012532	1 retrocopy	retro_nleu_84,
Ochotona princeps	ENSOPRG00000008875	2 retrocopies	retro_opri_1088 , retro_opri_21,
Tupaia belangeri	ENSTBEG00000001631	2 retrocopies	retro_tbel_3164, retro_tbel_3690,
Drosophila melanogaster	FBgn0035709	1 retrocopy	retro_dmel_68,